SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research
Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies h...
Gespeichert in:
| Veröffentlicht in: | PloS one 2012-07, Vol.7 (7), p.e35230-e35230 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e35230 |
|---|---|
| container_issue | 7 |
| container_start_page | e35230 |
| container_title | PloS one |
| container_volume | 7 |
| creator | Yu, Jian Xing, Xiaobin Zeng, Lingyao Sun, Jiehuan Li, Wei Sun, Han He, Ying Li, Jing Zhang, Guoqing Wang, Chuan Li, Yixue Xie, Lu |
| description | Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies have been performed to investigate the various levels of regulation. The resulting valuable data, however, remain scattered. Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple levels of research data available. Here we present a database for this purpose, SyStemCell, deposited with multi-level experimental data from stem cell research. The database currently covers seven levels of stem cell differentiation-associated regulatory mechanisms, including DNA CpG 5-hydroxymethylcytosine/methylation, histone modification, transcript products, microRNA-based regulation, protein products, phosphorylation proteins and transcription factor regulation, all of which have been curated from 285 peer-reviewed publications selected from PubMed. The database contains 43,434 genes, recorded as 942,221 gene entries, for four organisms (Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta) and various stem cell sources (e.g., embryonic stem cells, neural stem cells and induced pluripotent stem cells). Data in SyStemCell can be queried by Entrez gene ID, symbol, alias, or browsed by specific stem cell type at each level of genetic regulation. An online analysis tool is integrated to assist researchers to mine potential relationships among different regulations, and the potential usage of the database is demonstrated by three case studies. SyStemCell is the first database to bridge multi-level experimental information of stem cell studies, which can become an important reference resource for stem cell researchers. The database is available at http://lifecenter.sgst.cn/SyStemCell/. |
| doi_str_mv | 10.1371/journal.pone.0035230 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1325433773</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A477108329</galeid><doaj_id>oai_doaj_org_article_3fd4a1d576f2454e9dc15ceecf0efe94</doaj_id><sourcerecordid>A477108329</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-becd496fd067cf8b4e71d7eb5fc512447e9fd7fbd1c72b4baf1b9a80ea64e8063</originalsourceid><addsrcrecordid>eNqNk11vFCEUhidGY2v1HxglMTF6sSsMzDDjhUmz8aNJkyZWvSUMHHZpmGEEprb_XrY7bbqmF4YLCDzvezgHTlG8JHhJKCcfLvwUBumWox9giTGtSoofFYekpeWiLjF9fG99UDyL8QLjijZ1_bQ4KMsG87ZtDotwfn2eoF-Bcx-RRFom2ckIaPTj5GQCjf7YtEH95JIdHSAHl-Ai8gbB1QjB9jAk6W50yATfo5jdkMp2SFtjIORzK5P1AwoQQQa1eV48MdJFeDHPR8XPL59_rL4tTs--nqyOTxeqbsu06EBp1tZG45or03QMONEcusqoipSMcWiN5qbTRPGyY500pGtlg0HWDBpc06Pi9c53dD6KuVxREFpWjFLOaSZOdoT28kKMORsZroWXVtxs-LAWMiSrHAhqNJNEV7w2JasYtFqRSgEog8FAy7LXpzna1PWgVc47SLdnun8y2I1Y-0tBaVvXhGeDd7NB8L8niEn0Nm4LKQfwU743LjlmpKI4o2_-QR_ObqbWMidgB-NzXLU1FceMc4IbWraZWj5A5aGhtyr_LWPz_p7g_Z4gMwmu0lpOMYqT8-__z5792mff3mM3IF3aRO-m7d-J-yDbgSr4GAOYuyITLLatcVsNsW0NMbdGlr26_0B3otteoH8BJyIMQg</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1325433773</pqid></control><display><type>article</type><title>SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS)</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Yu, Jian ; Xing, Xiaobin ; Zeng, Lingyao ; Sun, Jiehuan ; Li, Wei ; Sun, Han ; He, Ying ; Li, Jing ; Zhang, Guoqing ; Wang, Chuan ; Li, Yixue ; Xie, Lu</creator><contributor>Stajich, Jason E.</contributor><creatorcontrib>Yu, Jian ; Xing, Xiaobin ; Zeng, Lingyao ; Sun, Jiehuan ; Li, Wei ; Sun, Han ; He, Ying ; Li, Jing ; Zhang, Guoqing ; Wang, Chuan ; Li, Yixue ; Xie, Lu ; Stajich, Jason E.</creatorcontrib><description>Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies have been performed to investigate the various levels of regulation. The resulting valuable data, however, remain scattered. Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple levels of research data available. Here we present a database for this purpose, SyStemCell, deposited with multi-level experimental data from stem cell research. The database currently covers seven levels of stem cell differentiation-associated regulatory mechanisms, including DNA CpG 5-hydroxymethylcytosine/methylation, histone modification, transcript products, microRNA-based regulation, protein products, phosphorylation proteins and transcription factor regulation, all of which have been curated from 285 peer-reviewed publications selected from PubMed. The database contains 43,434 genes, recorded as 942,221 gene entries, for four organisms (Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta) and various stem cell sources (e.g., embryonic stem cells, neural stem cells and induced pluripotent stem cells). Data in SyStemCell can be queried by Entrez gene ID, symbol, alias, or browsed by specific stem cell type at each level of genetic regulation. An online analysis tool is integrated to assist researchers to mine potential relationships among different regulations, and the potential usage of the database is demonstrated by three case studies. SyStemCell is the first database to bridge multi-level experimental information of stem cell studies, which can become an important reference resource for stem cell researchers. The database is available at http://lifecenter.sgst.cn/SyStemCell/.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0035230</identifier><identifier>PMID: 22807998</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Anopheles ; Biology ; Case studies ; Cell Differentiation ; Computer Science ; CpG islands ; Databases, Factual ; Databases, Genetic ; Deoxyribonucleic acid ; Differentiation (biology) ; DNA ; DNA Methylation ; Embryo cells ; Embryonic stem cells ; Embryonic Stem Cells - metabolism ; Embryos ; Experimental data ; Gene expression ; Gene Expression Regulation ; Gene regulation ; Genes ; Genetic analysis ; Histones - genetics ; Homo sapiens ; House mouse ; Humans ; Induced Pluripotent Stem Cells - metabolism ; Internet ; Kinases ; Macaca mulatta ; Macaca mulatta - genetics ; Mice ; MicroRNA ; MicroRNAs - genetics ; miRNA ; Mus musculus ; Neural stem cells ; Neural Stem Cells - metabolism ; Phosphorylation ; Pluripotency ; Proteins ; Rats ; Rattus norvegicus ; Regulatory mechanisms (biology) ; Ribonucleic acid ; RNA ; RNA, Messenger - genetics ; Software ; Stem cell research ; Stem cells ; Transcription (Genetics) ; Transcription Factors - genetics</subject><ispartof>PloS one, 2012-07, Vol.7 (7), p.e35230-e35230</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Yu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Yu et al. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-becd496fd067cf8b4e71d7eb5fc512447e9fd7fbd1c72b4baf1b9a80ea64e8063</citedby><cites>FETCH-LOGICAL-c692t-becd496fd067cf8b4e71d7eb5fc512447e9fd7fbd1c72b4baf1b9a80ea64e8063</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396617/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396617/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23864,27922,27923,53789,53791,79370,79371</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22807998$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Stajich, Jason E.</contributor><creatorcontrib>Yu, Jian</creatorcontrib><creatorcontrib>Xing, Xiaobin</creatorcontrib><creatorcontrib>Zeng, Lingyao</creatorcontrib><creatorcontrib>Sun, Jiehuan</creatorcontrib><creatorcontrib>Li, Wei</creatorcontrib><creatorcontrib>Sun, Han</creatorcontrib><creatorcontrib>He, Ying</creatorcontrib><creatorcontrib>Li, Jing</creatorcontrib><creatorcontrib>Zhang, Guoqing</creatorcontrib><creatorcontrib>Wang, Chuan</creatorcontrib><creatorcontrib>Li, Yixue</creatorcontrib><creatorcontrib>Xie, Lu</creatorcontrib><title>SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies have been performed to investigate the various levels of regulation. The resulting valuable data, however, remain scattered. Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple levels of research data available. Here we present a database for this purpose, SyStemCell, deposited with multi-level experimental data from stem cell research. The database currently covers seven levels of stem cell differentiation-associated regulatory mechanisms, including DNA CpG 5-hydroxymethylcytosine/methylation, histone modification, transcript products, microRNA-based regulation, protein products, phosphorylation proteins and transcription factor regulation, all of which have been curated from 285 peer-reviewed publications selected from PubMed. The database contains 43,434 genes, recorded as 942,221 gene entries, for four organisms (Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta) and various stem cell sources (e.g., embryonic stem cells, neural stem cells and induced pluripotent stem cells). Data in SyStemCell can be queried by Entrez gene ID, symbol, alias, or browsed by specific stem cell type at each level of genetic regulation. An online analysis tool is integrated to assist researchers to mine potential relationships among different regulations, and the potential usage of the database is demonstrated by three case studies. SyStemCell is the first database to bridge multi-level experimental information of stem cell studies, which can become an important reference resource for stem cell researchers. The database is available at http://lifecenter.sgst.cn/SyStemCell/.</description><subject>Analysis</subject><subject>Animals</subject><subject>Anopheles</subject><subject>Biology</subject><subject>Case studies</subject><subject>Cell Differentiation</subject><subject>Computer Science</subject><subject>CpG islands</subject><subject>Databases, Factual</subject><subject>Databases, Genetic</subject><subject>Deoxyribonucleic acid</subject><subject>Differentiation (biology)</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>Embryo cells</subject><subject>Embryonic stem cells</subject><subject>Embryonic Stem Cells - metabolism</subject><subject>Embryos</subject><subject>Experimental data</subject><subject>Gene expression</subject><subject>Gene Expression Regulation</subject><subject>Gene regulation</subject><subject>Genes</subject><subject>Genetic analysis</subject><subject>Histones - genetics</subject><subject>Homo sapiens</subject><subject>House mouse</subject><subject>Humans</subject><subject>Induced Pluripotent Stem Cells - metabolism</subject><subject>Internet</subject><subject>Kinases</subject><subject>Macaca mulatta</subject><subject>Macaca mulatta - genetics</subject><subject>Mice</subject><subject>MicroRNA</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Mus musculus</subject><subject>Neural stem cells</subject><subject>Neural Stem Cells - metabolism</subject><subject>Phosphorylation</subject><subject>Pluripotency</subject><subject>Proteins</subject><subject>Rats</subject><subject>Rattus norvegicus</subject><subject>Regulatory mechanisms (biology)</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Messenger - genetics</subject><subject>Software</subject><subject>Stem cell research</subject><subject>Stem cells</subject><subject>Transcription (Genetics)</subject><subject>Transcription Factors - genetics</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11vFCEUhidGY2v1HxglMTF6sSsMzDDjhUmz8aNJkyZWvSUMHHZpmGEEprb_XrY7bbqmF4YLCDzvezgHTlG8JHhJKCcfLvwUBumWox9giTGtSoofFYekpeWiLjF9fG99UDyL8QLjijZ1_bQ4KMsG87ZtDotwfn2eoF-Bcx-RRFom2ckIaPTj5GQCjf7YtEH95JIdHSAHl-Ai8gbB1QjB9jAk6W50yATfo5jdkMp2SFtjIORzK5P1AwoQQQa1eV48MdJFeDHPR8XPL59_rL4tTs--nqyOTxeqbsu06EBp1tZG45or03QMONEcusqoipSMcWiN5qbTRPGyY500pGtlg0HWDBpc06Pi9c53dD6KuVxREFpWjFLOaSZOdoT28kKMORsZroWXVtxs-LAWMiSrHAhqNJNEV7w2JasYtFqRSgEog8FAy7LXpzna1PWgVc47SLdnun8y2I1Y-0tBaVvXhGeDd7NB8L8niEn0Nm4LKQfwU743LjlmpKI4o2_-QR_ObqbWMidgB-NzXLU1FceMc4IbWraZWj5A5aGhtyr_LWPz_p7g_Z4gMwmu0lpOMYqT8-__z5792mff3mM3IF3aRO-m7d-J-yDbgSr4GAOYuyITLLatcVsNsW0NMbdGlr26_0B3otteoH8BJyIMQg</recordid><startdate>20120713</startdate><enddate>20120713</enddate><creator>Yu, Jian</creator><creator>Xing, Xiaobin</creator><creator>Zeng, Lingyao</creator><creator>Sun, Jiehuan</creator><creator>Li, Wei</creator><creator>Sun, Han</creator><creator>He, Ying</creator><creator>Li, Jing</creator><creator>Zhang, Guoqing</creator><creator>Wang, Chuan</creator><creator>Li, Yixue</creator><creator>Xie, Lu</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20120713</creationdate><title>SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research</title><author>Yu, Jian ; Xing, Xiaobin ; Zeng, Lingyao ; Sun, Jiehuan ; Li, Wei ; Sun, Han ; He, Ying ; Li, Jing ; Zhang, Guoqing ; Wang, Chuan ; Li, Yixue ; Xie, Lu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-becd496fd067cf8b4e71d7eb5fc512447e9fd7fbd1c72b4baf1b9a80ea64e8063</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Anopheles</topic><topic>Biology</topic><topic>Case studies</topic><topic>Cell Differentiation</topic><topic>Computer Science</topic><topic>CpG islands</topic><topic>Databases, Factual</topic><topic>Databases, Genetic</topic><topic>Deoxyribonucleic acid</topic><topic>Differentiation (biology)</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>Embryo cells</topic><topic>Embryonic stem cells</topic><topic>Embryonic Stem Cells - metabolism</topic><topic>Embryos</topic><topic>Experimental data</topic><topic>Gene expression</topic><topic>Gene Expression Regulation</topic><topic>Gene regulation</topic><topic>Genes</topic><topic>Genetic analysis</topic><topic>Histones - genetics</topic><topic>Homo sapiens</topic><topic>House mouse</topic><topic>Humans</topic><topic>Induced Pluripotent Stem Cells - metabolism</topic><topic>Internet</topic><topic>Kinases</topic><topic>Macaca mulatta</topic><topic>Macaca mulatta - genetics</topic><topic>Mice</topic><topic>MicroRNA</topic><topic>MicroRNAs - genetics</topic><topic>miRNA</topic><topic>Mus musculus</topic><topic>Neural stem cells</topic><topic>Neural Stem Cells - metabolism</topic><topic>Phosphorylation</topic><topic>Pluripotency</topic><topic>Proteins</topic><topic>Rats</topic><topic>Rattus norvegicus</topic><topic>Regulatory mechanisms (biology)</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA, Messenger - genetics</topic><topic>Software</topic><topic>Stem cell research</topic><topic>Stem cells</topic><topic>Transcription (Genetics)</topic><topic>Transcription Factors - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Jian</creatorcontrib><creatorcontrib>Xing, Xiaobin</creatorcontrib><creatorcontrib>Zeng, Lingyao</creatorcontrib><creatorcontrib>Sun, Jiehuan</creatorcontrib><creatorcontrib>Li, Wei</creatorcontrib><creatorcontrib>Sun, Han</creatorcontrib><creatorcontrib>He, Ying</creatorcontrib><creatorcontrib>Li, Jing</creatorcontrib><creatorcontrib>Zhang, Guoqing</creatorcontrib><creatorcontrib>Wang, Chuan</creatorcontrib><creatorcontrib>Li, Yixue</creatorcontrib><creatorcontrib>Xie, Lu</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yu, Jian</au><au>Xing, Xiaobin</au><au>Zeng, Lingyao</au><au>Sun, Jiehuan</au><au>Li, Wei</au><au>Sun, Han</au><au>He, Ying</au><au>Li, Jing</au><au>Zhang, Guoqing</au><au>Wang, Chuan</au><au>Li, Yixue</au><au>Xie, Lu</au><au>Stajich, Jason E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-07-13</date><risdate>2012</risdate><volume>7</volume><issue>7</issue><spage>e35230</spage><epage>e35230</epage><pages>e35230-e35230</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies have been performed to investigate the various levels of regulation. The resulting valuable data, however, remain scattered. Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple levels of research data available. Here we present a database for this purpose, SyStemCell, deposited with multi-level experimental data from stem cell research. The database currently covers seven levels of stem cell differentiation-associated regulatory mechanisms, including DNA CpG 5-hydroxymethylcytosine/methylation, histone modification, transcript products, microRNA-based regulation, protein products, phosphorylation proteins and transcription factor regulation, all of which have been curated from 285 peer-reviewed publications selected from PubMed. The database contains 43,434 genes, recorded as 942,221 gene entries, for four organisms (Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta) and various stem cell sources (e.g., embryonic stem cells, neural stem cells and induced pluripotent stem cells). Data in SyStemCell can be queried by Entrez gene ID, symbol, alias, or browsed by specific stem cell type at each level of genetic regulation. An online analysis tool is integrated to assist researchers to mine potential relationships among different regulations, and the potential usage of the database is demonstrated by three case studies. SyStemCell is the first database to bridge multi-level experimental information of stem cell studies, which can become an important reference resource for stem cell researchers. The database is available at http://lifecenter.sgst.cn/SyStemCell/.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22807998</pmid><doi>10.1371/journal.pone.0035230</doi><tpages>e35230</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2012-07, Vol.7 (7), p.e35230-e35230 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1325433773 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Anopheles Biology Case studies Cell Differentiation Computer Science CpG islands Databases, Factual Databases, Genetic Deoxyribonucleic acid Differentiation (biology) DNA DNA Methylation Embryo cells Embryonic stem cells Embryonic Stem Cells - metabolism Embryos Experimental data Gene expression Gene Expression Regulation Gene regulation Genes Genetic analysis Histones - genetics Homo sapiens House mouse Humans Induced Pluripotent Stem Cells - metabolism Internet Kinases Macaca mulatta Macaca mulatta - genetics Mice MicroRNA MicroRNAs - genetics miRNA Mus musculus Neural stem cells Neural Stem Cells - metabolism Phosphorylation Pluripotency Proteins Rats Rattus norvegicus Regulatory mechanisms (biology) Ribonucleic acid RNA RNA, Messenger - genetics Software Stem cell research Stem cells Transcription (Genetics) Transcription Factors - genetics |
| title | SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-14T00%3A42%3A11IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=SyStemCell:%20a%20database%20populated%20with%20multiple%20levels%20of%20experimental%20data%20from%20stem%20cell%20differentiation%20research&rft.jtitle=PloS%20one&rft.au=Yu,%20Jian&rft.date=2012-07-13&rft.volume=7&rft.issue=7&rft.spage=e35230&rft.epage=e35230&rft.pages=e35230-e35230&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0035230&rft_dat=%3Cgale_plos_%3EA477108329%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1325433773&rft_id=info:pmid/22807998&rft_galeid=A477108329&rft_doaj_id=oai_doaj_org_article_3fd4a1d576f2454e9dc15ceecf0efe94&rfr_iscdi=true |